"The thing that made him such a great runner may have killed him," Joe Shay told The Associated Press.
An enlarged heart like Ryan's is most commonly found in drinkers, smokers or people who are overweight, the father said. But it also translated into extra endurance - crucial for a distance runner.
Ryan and other top athletes underwent medical testing in Flagstaff, Ariz., where he trained, last spring, Joe Shay said, and he was cleared for running.
"He said the doctors told him that because your heart rate is so low, when you're older you may need a pacemaker to make adjustments on that," said Joe Shay, adding his son first was diagnosed with a larger than normal heart at age 14.
The 28-year-old Ryan Shay collapsed about 5½ miles into the race.
"I got a call that Ryan had fallen down ... then I got another call that his heart had stopped," Joe Shay said.
The medical examiner's office said an autopsy will be performed Sunday.
What was supposed to be a glorious weekend for the sport became instead a wake. That somber mood is sure to carry over to Sunday's New York City Marathon, in which 38,000 runners will compete.
"It's a big loss for the running community," said 2004 Olympic women's marathon bronze medalist Deena Kastor, who used to train with Shay in California. "It's a day we should be celebrating. It has cast a pall."
Shay and Ryan Hall and their wives had hoped to celebrate together after the trials. Now Hall is dedicating his race at the Olympics to Shay.
Minutes after Hall crossed the finish line first in record time, his arms raised in triumph, he heard the unthinkable news.
Shay was one of Hall's former training partners, and Shay's wife was Hall's teammate at Stanford.
"That just cut me straight to the heart," Hall said. "It makes you forget what you just did."
Organizers had decided to pair the trials with the storied annual marathon, hoping the timing would attract large crowds. The plan worked, as fans fought gusty wind to line the compact 26.2-mile course, which began in Rockefeller Center and traipsed through Times Square before heading to Central Park for five loops.
They witnessed a potentially historic day for American marathon running. Hall, a 25-year-old who had never raced the distance before April, established himself as a contender in Beijing, with a trials record time of 2 hours, 9 minutes, 2 seconds. Joining him in China will be Dathan Ritzenhein (2:11:07) and Brian Sell (2:11:40).
Meb Keflezighi, the 2004 Olympic silver medalist, was hobbled by cramps in both calves and fell back to eighth.
Keflezighi, 32, trained with Shay, reports CBS News correspondent Seth Doane.
"I thought he was going to have a breakthrough race, because he likes it when it's windy and tough conditions, it's him," said Keflezighi. "It's a really, really, really sad day, and I can't believe it. I cannot."
Shay hit the ground near the Central Park boathouse, a popular Manhattan tourist spot.
"He crossed right in front of me and stepped off the course," said runner Marc Jeuland of Chapel Hill, N.C., who did not see Shay collapse. "He nearly tripped me."
A statement from USA Track & Field said Shay immediately received CPR. He was taken to Lenox Hill Hospital, where he was pronounced dead on arrival at 8:46 a.m., according to New York City police.
A recreational runner died during last month's Chicago Marathon, the warmest in that event's history. But the death of an elite athlete during a major competition is a rare and startling occurrence.
On Friday, Hall and his wife, Sara, and Shay and his wife, Alicia, went for a run in Central Park. Shay seemed fine, Sara Hall said.
The Halls and Alicia were college teammates. Sara Hall considers Alicia one of her closest friends; she was a bridesmaid at the Shays' wedding in July.
It was in New York two years ago while watching the NYC marathon that Shay met his future wife. Alicia, who's hoping to make it to Beijing in the women's 10,000, was a two-time NCAA champion and the collegiate 10,000-meter record-holder while running as Alicia Craig at Stanford.
At the 2004 Olympic men's marathon trials, Shay was a favorite going in but was hampered by a hamstring strain and finished 23rd.
Shay was born May 4, 1979, in Ann Arbor, Mich., the fifth of eight children in a running family. His parents are the cross country and track coaches at Michigan's Central Lake High School.
"He achieved through hard work and effort goals and dreams that most people will never realize," Joe Shay said. "He was a champion, a winner and a good person. ... He used to say, 'Dad, there's a lot of guys out there with a lot more talent than me, but they will never outwork me."'
Watching an online interview of his son Friday night gave Joe Shay the urge to catch a 5 a.m. flight to New York and surprise him at Saturday's U.S. men's marathon Olympic trials.
He decided to stick with his original plan, to coach his runners in the Michigan state cross country meet.
"God, I regret it," he told The Associated Press on Saturday night. "I just do."
The dueling meets are a way of life for the Shay family. Ryan was the fifth of eight children, all runners. Joe and his wife, Susan, coach cross country and track at Central Lake High School.
Ryan encouraged his father to stay in Michigan with his athletes, saying, "Dad, you've been to these so many times."
At Notre Dame, Shay earned the school's first national individual track title with his victory in the NCAA 10,000 meters. Shay went on to become a five-time national road racing champion, winning the 2003 U.S. marathon, 2003 and 2004 half-marathon, 2004 20k and 2005 15k.
A moment of silence was observed for Shay, as well as for the recently slain brother of a Notre Dame football player, before Navy played Notre Dame in South Bend., Ind.
Susan Shay was in New York on Saturday night with two of Ryan's sisters and one of his brothers. Joe Shay was expected to leave Saturday night or Sunday morning.
None of the eight running Shay kids had ever suffered any serious injuries.
Running "dominated every moment of his time," Joe Shay said. Ryan also liked to fish and cut wood on property he owned in northern Michigan.
Ryan Shay had talked of becoming a chiropractor or a lawyer, his father said, because he could help people and stay involved with running.
When Ryan Shay was 14, he announced he would someday qualify for the Olympic trials. He was right.
He trained in Mammoth Lakes, Calif., with the Halls, Keflezighi and Kastor before moving to Flagstaff, Ariz.
"If you probably asked him if there was any way he wanted to go, it was out on the race course," said Terrence Mahon, who coached him in Mammoth.
Abdi Abdirahman, who dropped out of the marathon because of injury, trained with Shay for the past 3½ months in Flagstaff.
"I'm speechless. I still don't believe it," he said. "I probably was the last person to talk to him. We ate breakfast together, we ate lunch together, went to bed at the same time."
For Hall, Saturday culminated a reluctant route to the marathon. Neither Hall nor the second-place finisher, the 24-year-old Ritzenhein, had run a marathon as of a year ago. Saturday marked the second career race at the distance for both.
Hall broke away from the leading pack of five runners at about the 17th mile Saturday. He looked relaxed and fresh the entire race and was pumping his fist and bellowing over the final miles.
Too soon, those bellows became hushed words of shock and sympathy for Shay.
"He was a tremendous champion who was here today to pursue his dreams," said Craig Masback, CEO of USA Track & Field. "The Olympic trials is traditionally a day of celebration, but we are heartbroken."